Derar all,
I have recently moved from galaxy-central to galaxy-dist and all seems
to work fine except that everytime I start a new session (ie: I go to my
galaxy with my browser), I get the error below. I just need to reload
the page and all is fine again.
I would mention that while the whole 'dist' is original, the ./database/
directory is a mere copy (and updated) of the one I had in
galaxy-central. Needless to say that the MySQL engine is never down :)
Any help is most than welcome
Thanks a million!
Here's the error I get.
URL: http://galaxy.cbs.dtu.dk/galaxy/
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__
app_iter = self.application(environ, start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 111 in __call__
return self.app( environ, start_response )
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
134 in __call__
trans = self.transaction_factory( environ )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 187 in <lambda>
self.set_transaction_factory( lambda e: self.transaction_chooser( e,
galaxy_app, session_cookie ) )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 207 in transaction_chooser
return GalaxyWebUITransaction( environ, galaxy_app, self,
session_cookie )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 870 in __init__
self._ensure_valid_session( session_cookie )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 351 in _ensure_valid_session
self.app.model.GalaxySession.table.c.is_valid==True ) ) \
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py',
line 1300 in first
ret = list(self[0:1])
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py',
line 1221 in __getitem__
return list(res)
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py',
line 1361 in __iter__
return self._execute_and_instances(context)
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py',
line 1364 in _execute_and_instances
result = self.session.execute(querycontext.statement,
params=self._params, mapper=self._mapper_zero_or_none())
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py',
line 755 in execute
clause, params or {})
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py',
line 824 in execute
return Connection.executors[c](self, object, multiparams, params)
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py',
line 874 in _execute_clauseelement
return self.__execute_context(context)
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py',
line 896 in __execute_context
self._cursor_execute(context.cursor, context.statement,
context.parameters[0], context=context)
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py',
line 950 in _cursor_execute
self._handle_dbapi_exception(e, statement, parameters, cursor, context)
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py',
line 931 in _handle_dbapi_exception
raise exc.DBAPIError.instance(statement, parameters, e,
connection_invalidated=is_disconnect)
OperationalError: (OperationalError) (2006, 'MySQL server has gone
away') u'SELECT galaxy_session.id AS galaxy_session_id,
galaxy_session.create_time AS galaxy_session_create_time,
galaxy_session.update_time AS galaxy_session_update_time,
galaxy_session.user_id AS galaxy_session_user_id,
galaxy_session.remote_host AS galaxy_session_remote_host,
galaxy_session.remote_addr AS galaxy_session_remote_addr,
galaxy_session.referer AS galaxy_session_referer,
galaxy_session.current_history_id AS galaxy_session_current_history_id,
galaxy_session.session_key AS galaxy_session_session_key,
galaxy_session.is_valid AS galaxy_session_is_valid,
galaxy_session.prev_session_id AS galaxy_session_prev_session_id,
galaxy_session.disk_usage AS galaxy_session_disk_usage \nFROM
galaxy_session \nWHERE galaxy_session.session_key = %s AND
galaxy_session.is_valid = %s \n LIMIT 0, 1'
['ac609feb8dfe0f5669378398dde80af3', 1]
--
Federico De Masi, PhD,
Assistant Professor
The Technical University of Denmark - DTU
Center for Biological Sequence Analysis - CBS
Kemitorvet 208/002
DK-2800 KGS. LYNGBY, DENMARK
Telephone: (+45) 45 25 24 21
Fax: (+45) 45 93 15 85
http://rg.cbs.dtu.dk
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